Pharmaceutical strategies against amyloidosis: old and new drugs in targeting a "protein misfolding disease"

The group of diseases caused by abnormalities of the process of protein folding and unfolding is rapidly growing and includes diseases caused by loss of function as well as diseases caused by gain of function of misfolded proteins. Amyloidoses are caused by gain of function of certain proteins that lose their native structure and self-assemble into toxic insoluble, extracellular fibrils. This process requires the contribution of multiple factors of which only a few are established, namely the conformational modification of the amyloidogenic protein, protein's post-translational modifications and the co-deposition of glycosaminoglicans and of serum amyloid P component. In parallel with the exponential growth of biochemical data regarding the key events of the fibrillogenic process, several reports have shown that small molecules, through the interaction with either the amyloidogenic proteins or with the common constituents, can modify the kinetics of formation of amyloid fibrils or can facilitate amyloid reabsorption. These small molecules can be classified on the basis of their protein target and mechanism of action, according to the following properties. 1) molecules that stabilize the amyloidogenic protein precursor 2) molecules that prevent fibrillogenesis by acting on partially folded intermediates of the folding process as well as on low molecular weight oligomers populating the initial phase of fibril formation 3) molecules that interact with mature amyloid fibrils and weaken their structural stability 4) molecules that displace fundamental co-factors of the amyloid deposits like glycosaminoglycans and serum amyloid P component and favor the dissolution of the fibrillar aggregate.     

Aminoethylenes: a tetrahedral intermediate isostere yielding potent inhibitors of the aspartyl protease BACE-1

A series of novel beta-site amyloid precursor protein cleaving enzyme (BACE-1) inhibitors containing an aminoethylene (AE) tetrahedral intermediate isostere were synthesized and evaluated in comparison to corresponding hydroxyethylene (HE) compounds. Enzymatic inhibitory values were similar for both isosteres, as were structure-activity relationships with respect to stereochemical preference and substituent variation (P2/P3, P1, and P2'); however, the AE compounds were markedly more potent in a cell-based assay for reduction of beta-secretase activity. The incorporation of preferred P2/P3, P1, and P2' substituents into the AE pharmacophore yielded compound 7, which possessed enzymatic and cell assay IC(50)s of 26 nM and 180 nM, respectively. A three-dimensional crystal structure of 7 in complex with BACE-1 revealed that the amino group of the inhibitor core engages the catalytic aspartates in a manner analogous to hydroxyl groups in HE inhibitors. The AE isostere class represents a promising advance in the development of BACE-1 inhibitors.     

Serum amyloid P component: its role in platelet activation stimulated by sphingomyelinase D purified from the venom of the brown recluse spider (Loxosceles reclusa)

Serum amyloid P component or serum amyloid protein is a ubiquitous, highly conserved glycoprotein whose function is unknown. Although the related pentraxin, C-reactive protein, is an acute phase reactant in man, there is no direct evidence that human serum amyloid protein is involved in an inflammatory response. Here we show that serum amyloid protein is required by sphingomyelinase D, the principal necrotic agent of the venom of Loxosceles reclusa, for the in vitro-activation of human platelets. Furthermore, this platelet activation is dependent upon the presence of only serum amyloid protein; no other plasma components are necessary. Secretion of [3H]-serotonin and aggregation of platelets are nearly maximal following incubation of the platelets with purified sphingomyelinase D (0.3 micrograms/ml) and 5 micrograms/ml pure serum amyloid protein in the presence of calcium. Since the platelets are no longer activated when this 10% physiologic amount of serum amyloid protein is omitted, serum amyloid protein is likely to have a role in the necrosis caused by brown recluse spider venom.     

Characterization of recombinant, soluble beta-secretase from an insect cell expression system

The beta-site amyloid precursor protein-cleaving enzyme (BACE) cleaves the amyloid precursor protein to produce the N terminus of the amyloid beta peptide, a major component of the plaques found in the brains of Alzheimer's disease patients. Sequence analysis of BACE indicates that the protein contains the consensus sequences found in most known aspartyl proteases, but otherwise has only modest homology with aspartyl proteases of known three-dimensional structure (i.e., pepsin, renin, or cathepsin D). Because BACE has been shown to be one of the two proteolytic activities responsible for the production of the Abeta peptide, this enzyme is a prime target for the design of therapeutic agents aimed at reducing Abeta for the treatment of Alzheimer's disease. Toward this ultimate goal, we have expressed a recombinant, truncated human BACE in a Drosophila melanogaster S2 cell expression system to generate high levels of secreted BACE protein. The protein was convenient to purify and was enzymatically active and specific for cleaving the beta-secretase site of human APP, as demonstrated with soluble APP as the substrate in novel sandwich enzyme-linked immunosorbent assay and Western blot assays. Further kinetic analysis revealed no catalytic differences between this recombinant, secreted BACE, and brain BACE. Both showed a strong preference for substrates that contained the Swedish mutation, where NL is substituted for KM immediately upstream of the cleavage site, relative to the wild-type sequence, and both showed the same extent of inhibition by a peptide-based inhibitor. The capability to produce large quantities of BACE enzyme will facilitate protein structure determination and inhibitor development efforts that may lead to the evolution of useful Alzheimer's disease treatments.     

The role of heparan sulfate in the generation of Abeta

Alzheimer's disease is a fatal neurodegenerative disorder for which there are currently few treatments and no cure. Heparan sulfate, a heterogeneously sulfated glycosaminoglycan, has been identified as the first naturally occurring inhibitor of beta secretase, the rate-limiting step in the formation of Abeta, the peptide core of the amyloid plaques that cause Alzheimer's disease. Though heparan sulfate has frequently been implicated in the formation of fibrils, only fairly recently has its role as an inhibitor of beta secretase been recognized. This inhibitory activity is dependent on the structure and size of the heparan sulfate chain, with emphasis placed on the position of the sulfates. Heparan sulfate directly binds to beta secretase and causes a closed configuration of the catalytic site. Regulation of amyloid precursor protein (APP) beta secretase cleavage could occur at a number of cellular locations, including the Golgi complex, endosomal system and cell surface. Heparan sulfate also binds to APP and may sequester it away from beta secretase. These findings have led to the examination of heparan sulfate analogues, such as beta-secretase inhibitors, as a potential therapeutic approach to treat Alzheimer's disease.     

Beta-secretase (BACE) as a drug target for Alzheimer's disease

Evidence suggests that the beta-amyloid peptide (Abeta) is central to the pathophysiology of Alzheimer's Disease (AD). Amyloid plaques, primarily composed of Abeta, progressively develop in the brains of AD patients, and mutations in three genes (APP, PS1, and PS2) cause early on-set familial AD (FAD) by increasing synthesis of the toxic Abeta42 peptide. Given the strong association between Abeta and AD, therapeutic strategies to lower the concentration of Abeta in the brain should prove beneficial for the treatment of AD. Abeta is a proteolytic product of the large TypeI membrane protein, amyloid precursor protein (APP). Two proteases, called beta- and gamma-secretase, cleave APP to generate the Abeta peptide. For over a decade, the molecular identities of these proteases were unknown. Recently, the gamma-secretase has been tentatively identified as the presenilin proteins, PS1 and PS2, and the beta-secretase has been shown to be the novel transmembrane aspartic protease, beta-site APP Cleaving Enzyme 1 (BACE1; also called Asp2 and memapsin2). BACE2, a novel protease homologous to BACE1, was also identified, and the two BACE enzymes define a new family of transmembrane aspartic proteases. BACE1 exhibits all the properties of the beta-secretase, and as the key enzyme that initiates the formation of Abeta, BACE1 is an attractive drug target for AD. This review discusses the identification and initial characterization of BACE1 and BACE2, and summarizes our current understanding of BACE1 post-translational processing and intracellular trafficking. Finally, recent studies of BACE1 knockout mice, the BACE1 X-ray structure, and implications for BACE1 drug development will be discussed.     

Beta-secretase inhibition for the treatment of Alzheimer's disease--promise and challenge

As the number of cases of Alzheimer's disease (AD) rises in all developed countries, the unmet medical need for disease-modifying pharmacotherapy continues to grow. Much of AD research has been focused on the amyloid cascade hypothesis, which states that amyloid-beta-42 (A beta 42), a proteolytic derivative of the large transmembrane protein amyloid precursor protein (APP), plays an early and crucial role in all cases of AD. Consequently, blocking the production of A beta 42 by specific inhibition of the key proteases required for A beta 42 generation is a major focus of research into AD therapy. The identification of beta-secretase, the aspartic protease that generates the N-terminus of A beta 42, has triggered a race to develop drug-like inhibitors of this enzyme, which has become one of the major AD targets. Although the biology of beta-secretase holds great promise, it will be challenging to generate drug-like inhibitors of this unusual enzyme.     

2,2,2-Trifluoroethyl-thiadiazines: a patent evaluation of WO2016023927

The Alzheimer’s disease (AD) is acknowledged as the most common type of dementia in aging adults. It is characterized by the formation of intracellular neurofibrillary tangles and extracellular amyloid plaques. The latter insoluble deposits mainly consist of β-amyloid peptides (Aβ), which are the derivatives of the amyloid precursor protein (APP). The formation of neurotoxic Aβ-peptides involves the cleavage of APP with beta-secretase enzyme (beta-site APP cleaving enzyme 1, BACE1) so the potential of BACE1 inhibitors as therapeutic agents for AD is now drawing much attention.

The patent application WO2016023927 reports the preparation of new 1,2,4-thiadiazine inhibitors of BACE1 activity and their use as therapeutically active substances. Some of the new compounds are claimed to be good inhibitors with the IC₅₀ values in the 0.000292–0.134165 μM range. Several pharmaceutical preparations based on these compounds are proposed for possible treatment and prevention of AD.

Expert opinion: In light of the novelty from the chemical point of view and improved biological activity, the reported 2,2,2-trifluoroethylthiadiazines could be considered as promising BACE1 inhibitors. However, the available data are insufficient to make a recommendation if these compounds can be considered as drug candidates. Further studies with a larger number of compounds are required. The compounds described in the patent have to be characterized more thoroughly from the chemical viewpoint (e.g., by means of IR, ¹H and ¹³C NMR spectroscopy, X-ray crystallography), especially as regards stereochemical details.     

The search for drug leads targeted to the beta-secretase: an example of the roles of computer assisted approaches in drug discovery

The inhibition of beta-secretase has become a very promising approach to control the onset and progression of Alzheimer's disease due to its involvement in the generation of amyloid plaques. The main goal of the many drug discovery projects targeting this enzyme is the identification of highly specific, non-peptidic compounds with low molecular weight, characteristics that are desirable for drug leads with low toxicity that have to transverse the blood brain barrier. We describe the main approaches used in the discovery of novel inhibitors, including substrate specificity, target structure based design, and high throughput screening (HTS), both in vitro and in silico. We place special emphasis in the receptor based design and in silico HTS, two strategies that make wide use of computer assisted tools. To exemplify the usefulness and versatility of computer tools in this endeavor we use the computer generated 'enzyme's binding site cast' to rationalize qualitatively some salient structural features of known beta-secretase second generation inhibitors, and for guiding the review of many of the ligands whose complexes with the enzyme have been studied by X-ray crystallography. We discuss the use made by other authors of molecular modelling for the understanding of the very special characteristics of ligand binding to beta-secretase and for the design of new inhibitors. Finally, we review the quest for non-peptidic inhibitors that has led to the use of HTS in vitro and in silico. The screening of extensive libraries resulted in a few low affinity compounds that do not fit into the key S1/S1' pockets, indicating that this is not an easy target to block.     

Protein conformational diseases: from mechanisms to drug designs

Amyloidosis comprises a group of diseases characterized by the deposition of insoluble protein fibrils in specific organs and includes several serious medical disorders, such as Alzheimer's disease, prion-associated transmissible spongiform encephalitis, and type II diabetes. Despite the structural dissimilarity between the soluble proteins and peptides, these fibrils exhibit similar morphologies under electron microscopy with a characteristic "cross beta-sheet" pattern examined by x-ray fiber diffraction experiments. Many studies have revealed that each of these diseases is associated to a specific protein that is partially unfolded, misfolded, and aggregated. However, the detailed structures of the causative agents and the toxicity mechanisms are less known. This review summarizes recent studies in the conformational disorders leading to aggregation; including which proteins potentially cause conformational diseases, the aggregation mechanisms of these proteins, and recent researches on the conformational changes using advanced experiments or molecular dynamics simulations. Finally, current drug designs towards these protein conformational diseases are also discussed. It is believed that the advances in basic understanding of the mechanisms of conformational changes as well as biological functions of these proteins will shed light on the development and design of potential interfering compounds against amyloid formation associated with protein conformational diseases.     

A false paradise - mixed blessings in the protein universe: the amyloid as a new challenge in drug development

Significant advances in therapeutic applications of proteins and peptides have brought new challenges in the field of drug development. Ordered protein aggregation known as amyloid formation has recently emerged as a universal phenomenon due to extensive research in protein folding and amyloid diseases. The amyloid represents a new generic structure characterized by cross-beta-sheet formation in its core, which implies that any polypeptide can adopt this conformation under amyloid-prone conditions. Some widely-used biopharmaceuticals such as insulin, glucagon, amylin and calcitonin have been shown to form amyloids and this list may be significantly extended upon further research. Compared to soluble precursor proteins and amorphous aggregates amyloids gain new properties such as remarkable stability and protease resistance, polymorphism, self-propagation via seeding and cross-seeding, cytotoxicity and induced immunogenicity. Some of them can be hazardous in biopharmaceutical applications. The causes of amyloid aggregation and strategies for its prevention are reviewed here. They utilize the current knowledge of amyloid properties, structure-based design principles and protein chemistry. Once these challenges are met, they will ultimately lead to safer and surer pharmaceuticals.     

Inhibition of angiogenesis and tumor growth by beta and gamma-secretase inhibitors

The involvement of beta-secretase and gamma-secretase in producing the beta-amyloid component of senile plaques found in the brain of Alzheimer's patients has fueled a major research effort to design selective inhibitors of these proteases. Interestingly, gamma-secretase cleaves several proteins including Notch, E-cadherin, CD44 and ErbB-4 (erythroblastic leukemia viral oncogene homolog 4), which are important modulators of angiogenesis. The beta-amyloid precursor protein, which is cleaved by beta-secretase and gamma-secretase to produce beta-amyloid, is highly expressed in the endothelium of neoforming vessels suggesting that it might play a role during angiogenesis. These data prompted us to explore the effects of beta and gamma-secretase inhibitors of different structures on angiogenesis and tumor growth. Both the gamma and beta-secretase inhibitors tested reduce endothelial cell proliferation without inducing cellular toxicity, suppress the formation of capillary structures in vitro and oppose the sprouting of microvessel outgrowths in the rat aortic ring model of angiogenesis. Moreover, they potently inhibit the growth and vascularization of human glioblastoma and human lung adenocarcinoma tumors xenotransplanted into nude mice. Altogether these data suggest that the gamma and beta-secretases play an essential role during angiogenesis and that inhibitors of the beta and gamma-secretases may constitute new classes of anti-angiogenic and anti-tumoral compounds.     

Human beta-secretase (BACE) and BACE inhibitors: progress report

A key step in the processing of the integral membrane protein APP, or Amyloid Precursor Protein is through the proteolytic cleavage by the enzyme beta-Secretase (BACE). The proteolysis of APP by BACE, followed by subsequent C-terminal cleavage(s) by gamma-secretase, results in the formation of the amyloid beta (Abeta) peptide. The principal component of the neuritic plaque found in the brains of Alzheimer's Disease (AD) patients is Abeta which is a neurotoxic and highly aggregatory peptide segment of APP. The amyloid hypothesis holds that the neuronal dysfunction and clinical manifestation of AD is a consequence of the long term deposition and accumulation of 40-42 amino-acid long Abeta peptides, and that this process leads to the onset and progression of AD. Due to the apparent causal relationship between Abeta and AD, the so-called "secretases" that produce Abeta have been targeted for development of inhibitors that might serve as therapeutic agents for treatment of this dreaded, and ever more prevalent disease. Herein will be discussed our current understanding of BACE, its role in the formation of neuritic plaques and the known inhibitors of the enzyme.     

Genetic basis of neurodegeneration in familial Alzheimer's disease

Alzheimer's disease (AD), the most common form of dementia, is characterized by two types of brain lesions, referred to as senile plaques and neurofibrillary tangles. Moreover, neuronal cell loss and synaptic degeneration appear in affected regions of the brain. A series of endoproteolytic cleavages of the amyloid precursor protein (APP) controlled by alpha, beta, and gamma-secretases leads to a formation of non-amyloidogenic (the alpha-secretase pathway) and amyloidogenic (the beta-secretase pathway) products which are essential for neurodegeneration. According to the "amyloid cascade hypothesis", the accumulation of amyloid beta (Abeta) peptides in the brain is a primary event in the pathogenesis of AD. One of the strong pieces of evidence supporting this hypothesis was the identification of pathogenic mutations within APP, presenilin 1 and presenilin 2 genes responsible for familial autosomal dominant AD. These mutations affect APP processing causing overproduction of Abeta42. Finding specific inhibitors of the Abeta42 generation is a major goal of AD drug development programs now and the key challenge for the treatment of the most devasting disease of human brain.     

Amyloid associated proteins in Alzheimer's and prion disease

Clustering of activated microglia in Abeta deposits is related to accumulation of amyloid associated factors and precedes the neurodegenerative changes in AD. Microglia-derived pro-inflammatory cytokines are suggested to be the driving force in AD pathology. Inflammation-related proteins, including complement factors, acute-phase proteins, pro-inflammatory cytokines, that normally are locally produced at low levels, are increasingly synthesized in Alzheimer's disease (AD) brain. Similar to AD, in prion diseases (Creutzfeldt-Jakob disease, Gerstmann-Str?ussler-Scheinker disease and experimentally scrapie infected mouse brain) amyloid associated factors and activated glial cells accumulate in amyloid deposits of conformational changed prion protein (PrPres). Biological properties of Abeta and prion (PrP) peptides, including their potential to activate microglia, relate to Abeta and PrP peptide fibrillogenic abilities that are influenced by certain amyloid associated factors. However, since small oligomers of amyloid forming peptides are more toxic to neurons than large fibrils, certain amyloid associated factors that enhance fibril formation, may sequester the potentially harmful Abeta and PrP peptides from the neuronal microenvironment. In this review the positive and negative actions of amyloid associated factors on amyloid peptide fibril formation and on the fibrillation state related activation of microglia will be discussed. Insight in these mechanisms will enable the design of specific therapies to prevent neurodegenerative diseases in which amyloid accumulation and glial activation are prominent early features.     

Macrocyclic inhibitors of beta-secretase: functional activity in an animal model

A macrocyclic inhibitor of beta-secretase was designed by covalently cross-linking the P1 and P3 side chains of an isophthalamide-based inhibitor. Macrocyclization resulted in significantly improved potency and physical properties when compared to the initial lead structures. More importantly, these macrocyclic inhibitors also displayed in vivo amyloid lowering when dosed in a murine model.     

Construction of a small peptide library related to inhibitor OM99-2 and its structure-activity relationship to β-secretase

AIM: To develop probes for detecting the binding specificity between beta-secretase and substrate, and provide reliable biological activity data for further researching encircling substrate-based inhibitors. METHODS: To prepare the inhibitors, the hydroxyethylene (HE) segment including P1 and P1'was synthesized after multi-step reactions; the combination of all segments was then completed through solid phase synthesis. Recombinant human beta-secretase ectodomain (amino acid residues 1-460) was expressed as a secreted protein with a C-terminal His tag in insect cells using baculovirus infection, and all compounds were evaluated in this beta-secretase enzyme assay. In order to understand the interaction in detail, the theoretical methods, namely molecular dynamics (MD) simulation and molecular mechanics-generalized-born surface area (MM-GBSA) analysis, were performed on the complex of beta-secretase and OM99-2 to obtain the geometrical and energetical information. RESULTS: We designed and constructed a positional scanning combinatorial library including 16 compounds; all members of the library were synthesized based on HE dipeptide isostere. Structure-activity relationship studies at the P4-P1 and P1' -P4'positions led to the discoveries of P and P'sides binding specificity and potent inhibitors 14, 18, and 22. The binding free energy on the whole system and every residue were compared to the biological assay result. CONCLUSION: The removal of P4' yielded inhibitor 22 (A3 *B2) with high potency; further truncation of P3'gave inhibitor 18 (A3 *B1) with equal activity, implying that the right side of the inhibitors play a less important role and could be easily simplified, while change on the P side may cause substantial results.     

Progress in the discovery of BACE inhibitors

Dementia caused by Alzheimer's disease is a large medical burden on society in the developed world. Current treatments are largely symptomatic, and there is an urgent need for therapies which can interrupt or reverse the progression of disease. A number of strategies for intervention are being actively pursued; among the most promising is the inhibition of beta-secretase, or BACE. BACE is the enzyme responsible for N-terminal cleavage of the Alzheimer's precursor protein leading to the production of the beta-amyloid peptide. This cascade ultimately leads to the formation of amyloid plaques, one of the hallmark lesions of the disease. It is expected that inhibitors of BACE may therefore serve as an effective disease-modifing therapy for the treatment of AD. This concept has received significant attention by both academics and the pharmaceutical industry. This review focuses on a discussion of the reported structure-activity relationships for inhibitors of this important therapeutic target.     

Benzofuranone derivatives as effective small molecules related to insulin amyloid fibrillation: a structure-function study

Amyloids are protein fibrils of nanometer size resulting from protein self-assembly. They have been shown to be associated with a wide variety of diseases such as Alzheimer's and Parkinson's and may contribute to various other pathological conditions, known as amyloidoses. Insulin is prone to form amyloid fibrils under slightly destabilizing conditions in vitro and may form amyloid structures when subcutaneously injected into patients with diabetes. There is a great deal of interest in developing novel small molecule inhibitors of amyloidogenic processes, as potential therapeutic compounds. In this study, the effects of five new synthetic benzofuranone derivatives were investigated on the insulin amyloid formation process. Protein fibrillation was analyzed by thioflavin-T fluorescence, Congo red binding, circular dichroism, and electron microscopy. Despite high structural similarity, one of the five tested compounds was observed to enhance amyloid fibrillation, while the others inhibited the process when used at micromolar concentrations, which could make them interesting potential lead compounds for the design of therapeutic antiamyloidogenic compounds.